So I've read a lot of posts here trying to troubleshoot my problem, which is a bogging and coughing behavior when opening the throttle while parked. This behavior did not occur before opening the airbox and adding open pipes. While the choke is out the throttle revs normal, however once it's warm the throttle response is crap. The bike seems to start ok when cold, idles decently.

My first thought was an air leak. I sprayed WD-40 around the engine intake and carb intake and didn't notice a change in idle. However I noticed some bubbling around the rubber intake manifold (some very visible cracking). I replaced both and idle is better but the throttle still bogs.

Next thought was the ignition coil, which failed last year on a long road trip through hot Texas. I tested the spark plug caps with a multimeter and got a reading of 13 kOhms. I read that the normal range for the carb'd models is between 18-20 kOhms. Is this far enough off spec to cause this bogging?

What else might be the problem here? Do I need to rejet? Spark plugs are pretty clean and recently gapped. 22,000 miles on the bike, not sure about valve clearances. I'm looking forward to getting the bike running again so I can rip around with these new mods. I could also try posting an audio clip of the bogging/coughing if that would be helpful.

Just perusing the available info on the 790 if you are using the stock needle you need to be 140+ if using the thrux needle 125+ you will need 1 or 2 shims and might well need to up to 42 on the pilots. Turns is what she needs 2.5 - 3.0.
A balance will be in order after the mods.

There is a lean bog and a rich bog, they are both a little different but with your setup and 130 mains, it won't be a rich bog. Try 135-138 mains and one shim under the needle, if the bogging is still there try 2 shims and see how it feels.

135 mains, 2 shims, 3.25 turns, great idle and no more bogging. Took it for a ride and really put it through it's rpms. Lots of power in the mid range, easily whipped my head back in 3rd gear going about 45mph. I did notice that the bottom end is a bit weaker than I would expect. Opening up the throttle in 1st and 2nd gear from low rpms makes a lot of noise but not as much pick-up. Any thoughts?

135 mains, 2 shims, 3.25 turns, great idle and no more bogging. Took it for a ride and really put it through it's rpms. Lots of power in the mid range, easily whipped my head back in 3rd gear going about 45mph. I did notice that the bottom end is a bit weaker than I would expect. Opening up the throttle in 1st and 2nd gear from low rpms makes a lot of noise but not as much pick-up. Any thoughts?

I also have a scarlet/silver 2001 with similar mods. The only differences are I did the Bella Corsa DIY airbox removal kit kit and I have TORS. I'm running 135 mains, 42 pilots, Thruxton needles with one shim and about 2.5 turns. I'm pretty happy with that tuning. The Thruxton needles seem to be a good $20 investment.

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